I now read out the vsm_settings.yaml using (the VSMSettings load function is defined in VortexStepMethod.jl)

vsm_settings = VSMSettings("pyramid_model/vsm_settings.yaml")

Instead of defining the vsm_settings.yaml path inside the system.yaml.

Then inside vsm_settings.yaml I point to: aero_geometry.yaml

# Define wing geometry files and discretization parameters
wings:
    - name: V3_Kite                    # Wing identifier for output labeling
      geometry_file: data/TUDELFT_V3_KITE/aero_geometry.yaml

This is a bit of a nested approach, whereas the "ideal" way would be to point to vsm_settings.yaml and aero_geometry.yaml inside system.yaml.

Is this crucial? And, how could I achieve this?

BTW:
Loading from a sub-directory works, so a folder PROJECT_DIR/data/sub_dir/system.yaml
Can be read using

set = Settings("sub_dir/system.yaml")